Contacts of the helix formed by residues 61 - 71 (chain B) in PDB entry 2FIU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 3.9 27.3 - - - +
2B ALA 3.4 13.9 - - - -
4B GLY* 3.5 8.3 + - - +
59B PHE* 3.1 8.3 + - - +
60B PRO* 1.3 82.3 - - - +
62B VAL* 1.3 63.8 + - - +
63B GLN* 3.3 10.3 + - - +
64B HIS* 2.9 33.1 + - - +
65B ALA 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 5.6 0.7 - - - +
44A THR* 4.4 7.4 - - - +
1B MSE 5.6 0.8 - - - +
2B ALA 4.1 2.7 + - - +
3B LYS 4.2 0.4 - - - +
4B GLY* 3.7 15.5 - - - +
61B SER* 1.3 71.9 - - - +
63B GLN* 1.3 59.5 + - - +
65B ALA* 2.9 5.0 + - - +
66B ILE* 2.8 48.9 + - + +
91B ILE* 4.2 15.3 - - + -
93B GLU* 3.7 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 5.5 7.1 - - + +
61B SER* 3.2 9.5 + - - +
62B VAL* 1.3 81.6 - - - +
64B HIS* 1.3 56.5 + - + +
66B ILE* 3.8 23.4 - - - +
67B ASP* 2.7 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.5 35.1 + - - +
59B PHE* 4.0 2.9 - - + -
60B PRO* 3.7 33.1 - - + +
61B SER* 2.9 46.7 + - - +
63B GLN* 1.3 76.7 - - + +
65B ALA* 1.3 57.4 + - - +
67B ASP* 3.6 4.9 + - - -
68B CYS* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 4.9 1.6 - - - -
6B TRP* 3.6 8.9 - - + -
59B PHE* 3.5 35.6 - - + -
61B SER 3.2 6.7 + - - +
62B VAL 2.9 8.8 + - - +
64B HIS* 1.3 76.2 - - - +
66B ILE* 1.3 58.9 + - - +
68B CYS* 3.3 3.3 + - - +
69B TYR* 3.0 24.8 + - - +
91B ILE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 4.0 23.3 - - + +
46A LEU* 5.3 2.5 - - + -
62B VAL* 2.8 41.6 + - + +
63B GLN* 3.8 26.0 - - - +
65B ALA* 1.3 70.5 - - - +
67B ASP* 1.3 62.9 + - - +
69B TYR* 3.3 5.9 + - - +
70B ASN* 2.9 46.0 + - - +
91B ILE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.5 26.4 - - + -
63B GLN* 2.7 53.1 + - - +
64B HIS* 3.9 2.7 - - - +
66B ILE* 1.3 74.6 - - - +
68B CYS* 1.3 60.8 + - - +
70B ASN* 3.3 6.8 + - - +
71B SER* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TRP* 4.1 6.1 - - - -
28B ALA* 3.7 29.2 - - - -
29B PHE* 3.7 28.9 - - - -
32B PHE* 3.6 21.9 - - + -
59B PHE* 3.8 13.9 - - + -
64B HIS 3.0 18.5 + - - +
65B ALA 3.5 5.4 - - - +
66B ILE 3.2 0.2 - - - -
67B ASP* 1.3 76.6 - - - +
69B TYR* 1.3 61.3 + - - +
71B SER* 2.6 24.4 + - - -
74B TYR* 3.1 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.5 56.3 + - + -
47A GLU* 2.7 40.2 + - - +
6B TRP* 3.6 20.7 - + + -
65B ALA 3.0 9.3 + - - +
66B ILE 3.3 8.3 + - - +
68B CYS* 1.3 76.4 - - - +
70B ASN* 1.3 69.7 + - - +
71B SER 3.6 0.2 + - - -
74B TYR* 3.5 33.0 - + - +
75B GLN* 2.8 45.6 + - - +
78B ALA* 5.3 1.1 - - + -
81B ARG* 4.5 1.3 - - - -
82B GLN* 4.4 3.8 + - - -
89B MSE 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.9 36.4 + - - +
67B ASP* 3.6 7.6 + - - +
68B CYS 3.2 0.2 - - - -
69B TYR* 1.3 89.6 - - - +
71B SER* 1.3 66.4 + - - +
72B PRO* 3.6 2.6 - - - +
75B GLN* 3.8 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 3.6 7.7 - - - +
31B ARG* 3.9 1.8 - - - -
32B PHE* 3.9 18.4 - - - -
67B ASP 2.9 12.6 + - - -
68B CYS* 2.6 21.7 + - - -
70B ASN* 1.3 79.6 - - - +
72B PRO* 1.4 78.1 - - - +
73B GLU* 3.6 9.6 - - - -
74B TYR* 3.1 16.5 + - - +
75B GLN* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il